Ordinal Questions Logistic Regression

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require(foreign)
library(foreign)
require(ggplot2)
require(MASS)
require(Hmisc)
require(reshape2)
library(stringr)
library(rlist)
library(rlang)
library(dplyr)

df <- (read.csv(file = 'ordinal_questions.csv'))
df$sex <- factor(df$sex)
df$bowel <- factor(df$bowel)
#levels(df$bowel) <- c(4,2,3,1)

drop <- c('assessment.digestion.bowel.movements.enum','assessment_vitals_supplements_text','assessment.vitals.supplements.text','assessment.vitals.adopted.enum','new.health.history.is.remapped','old.health.history.is.remapped','assessment.health.history.biological_sex.int','diabetes')
df <- df[,!(names(df)) %in% drop]
df[df == ""] <- NA

#col_names <- c(names(df)[2:18],names(df)[26:90],names(df)[96:140])
#df[col_names] <- lapply(df[col_names], factor)
#df

df$laxatives <- factor(df$laxatives, levels = c("(4) Not at all","(3) Once per week or less","(2) Several times per week","(1) Daily"), labels = c("(1) Not at all","(2) Once per week or less","(3) Several times per week","(4) Daily"))


df$assessment.digestion.bloating.enum <- factor(df$assessment.digestion.bloating.enum, levels = c("(4) Infrequently or not at all","(3) Once per week or less","(2) Several times per week", "(1) Daily"), labels = c("(1) Infrequently or not at all","(2) Once per week or less","(3) Several times per week","(4) Daily"))

df$assessment.digestion.poor_or_lack_of_appetite.enum <- factor(df$assessment.digestion.poor_or_lack_of_appetite.enum, levels = c("(3) No","(2) Occasionally (once a week or less)","(1) Regularly (daily or several times per week)"), labels = c("(1) No","(2) Occasionally (once a week or less)","(3) Regularly (daily or several times per week)"))


df[,'assessment.personality.irritated_easily.enum'] <- factor(df[,'assessment.personality.irritated_easily.enum'], levels = c("(1) Strongly agree", "(2) Agree", "(3) Neither disagree nor agree", "(4) Disagree", "(5) Strongly disagree"), labels = c("(5) Strongly agree", "(4) Agree", "(3) Neither disagree nor agree", "(2) Disagree", "(1) Strongly disagree"))


df[,'assessment.personality.often_blue.enum'] <- factor(df[,'assessment.personality.often_blue.enum'] , levels = c("(1) Strongly agree", "(2) Agree", "(3) Neither disagree nor agree", "(4) Disagree", "(5) Strongly disagree"), labels = c("(5) Strongly agree", "(4) Agree", "(3) Neither disagree nor agree", "(2) Disagree", "(1) Strongly disagree"))

df$ab_pain <- factor(df$ab_pain, levels = c("(4) Not at all","(3) Less than weekly","(2) More than 1 time per week","(1) Daily"), labels = c("(1) Not at all","(2) Less than weekly","(3) More than 1 time per week","(4) Daily"))

df$exercise <- factor(df$exercise, levels = c("(5) Rarely or never","(4) Less than once per week","(3) 1-2 times per week","(2) At least 3 times a week","(1) At least 5 times a week","(0) At least 7 times per week"), labels = c("(0) Rarely or never","(1) Less than once per week","(2) 1-2 times per week","(3) At least 3 times a week","(4) At least 5 times a week", "(5) At least 7 times per week"))

df[,'assessment.lifestyle.cruciferous_vegetables.enum'] <- factor(df[,'assessment.lifestyle.cruciferous_vegetables.enum'], levels = c("(0) Daily","(1) 3-4 times per week","(2) Once per week","(3) Once per month","(4) Less than once per month"), labels = c("(4) Daily","(3) 3-4 times per week","(2) Once per week","(1) Once per month","(0) Less than once per month"))

df[,'assessment.lifestyle.breakfast.enum'] <- factor(df[,'assessment.lifestyle.breakfast.enum'], levels = c("(0) Daily","(1) 3-4 times per week","(2) Once per week","(3) Once per month","(4) Less than once per month"), labels = c("(4) Daily","(3) 3-4 times per week","(2) Once per week","(1) Once per month","(0) Less than once per month"))

df[,'assessment.digestion.gas.enum'] <- factor(df[,'assessment.digestion.gas.enum'], levels = c("(1) Daily","(2) Several times per week","(3) Once per week or less","(4) Infrequently or not at all"), labels = c("(4) Daily","(3) Several times per week","(2) Once per week or less","(1) Infrequently or not at all"))


df[,'assessment.digestion.diarrhea.enum'] <- factor(df[,'assessment.digestion.diarrhea.enum'], levels = c("(1) Daily","(2) Several times per week","(3) Once per week or less","(4) Infrequently or not at all"), labels = c("(4) Daily","(3) Several times per week","(2) Once per week or less","(1) Infrequently or not at all"))

df$assessment.lifestyle.vigorous_activity.enum <- factor(df$assessment.lifestyle.vigorous_activity.enum, levels = c("(5) Rarely or never","(4) Less than once per week","(3) 1-2 times per week","(2) At least 3 times a week","(1) At least 5 times a week"), labels = c("(1) Rarely or never","(2) Less than once per week","(3) 1-2 times per week","(4) At least 3 times a week","(5) At least 5 times a week"))

df$assessment.digestion.acid_reflux.enum <- factor(df$assessment.digestion.acid_reflux.enum, levels = c("(4) Not at all","(3) Less than weekly","(2) More than 1 per week","(1) Daily"), labels = c("(1) Not at all","(2) Less than weekly","(3) More than 1 per week","(4) Daily"))

df$assessment.satisfaction.rarely_rested.enum <- factor(df$assessment.satisfaction.rarely_rested.enum, levels = c("(6) Strongly Disagree","(5) Moderately Disagree","(4) Slightly Disagree","(3) Slightly Agree","(2) Moderately Agree","(1) Strongly Agree"), labels = c("(1) Strongly Disagree","(2) Moderately Disagree","(3) Slightly Disagree","(4) Slightly Agree","(5) Moderately Agree","(6) Strongly Agree"))

#convert character columns to factors
df[,c(15:ncol(df))][sapply(df[,c(15:ncol(df))], is.character)] <- lapply(df[,c(15:ncol(df))][sapply(df[,c(15:ncol(df))], is.character)], 
                                       as.factor)
df <- df %>%
  select(c('public_client_id','bowel','sex','age','BMI_CALC','eGFR'), everything())
df

levels(df[,'ab_pain'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.joyful.moments.feel_empowered.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.satisfaction.rarely_rested.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.personality.irritated_easily.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.satisfaction.rarely_rested.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.personality.often_blue.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.lifestyle.vegetables.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.lifestyle.water.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.lifestyle.cruciferous_vegetables.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.lifestyle.breakfast.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.diet.freq_cook_home.int'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.diet.freq_raw_vegetables_salad.int'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.lifestyle.sugary_drinks.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'exercise'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.lifestyle.alcohol_days_a_week.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.digestion.bowel.movement.completion.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'laxatives'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.digestion.diarrhea.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.digestion.bloating.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.health.history.drugs_cholesterol.int'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.digestion.poor_or_lack_of_appetite.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'assessment.digestion.gas.enum'])

[1] "1" "2" "3" "4" "5"

levels(df[,'bowel_ease'])

[1] "1" "2" "3" "4" "5"

(str(unique(df[,'assessment.joyful.moments.feel_empowered.enum'])))

 Factor w/ 5 levels "1","2","3","4",..: 2 4 3 1 5 NA
NULL

c(unname(unlist(newlevels)))

[1] 1 2 3 4 5

newlevels = list()
newlabels = list()
test[,col] <- df[,'assessment.personality.irritated_easily.enum']
list_contents <- levels(test[,col])[which(!(is.na(levels(test[,col])) & is_empty(any(levels(test[,col]))) & identical(any(levels(test[,col])),character(0))))]

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

chars <- seq(0,length(list_contents))
 if(!is.character(test[,col]) & !is.double(test[,col]) & length(levels(test[,col])[which(!is.na(levels(test[,col])))][which(str_detect(!(is.na(any(levels(test[,col]))) & is_empty(any(levels(test[,col]))) & identical(any(levels(test[,col])),character(0))), paste0("(",any(chars),")",sep="")))]) != 0) {
    print(paste0("factored column detected: ",'assessment.personality.irritated_easily.enum',sep=""))
    print(paste0("Testing character: ",chars,sep=""))
    list2<-list()
    for (i in seq(1,length(list_contents))) {
      list2<-list()
      char_name <- i
      list_item <- paste0(list_contents[which(str_detect(!(is.na(list_contents) & is_empty(list_contents) & identical(list_contents,character(0))), paste0("(",any(chars),")",sep="")))][i],sep="")
      if (!is.na(list_item)) {
        list1 <- as.numeric(char_name)
        names(list1) <- list(char =  list_item)
        list2 <- list.append(c(list(char = list_item),list2))
        names(list2) <- list(char =  names(list1))
        newlevels <- list.append(c(list1,newlevels))
        newlabels <- list.append(c(list2,newlabels))
      }
    }
  }

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"

  if (any(str_detect(list_item,paste0(c(3:9),sep="")))) {
    for (j in seq(0,length(newlabels))) {
      newlabels %>%
        str_replace_all(paste0(length(newlabels)-j),newlabels[j],paste0(j+1))
    }
  }
  print(unname(unlist(newlabels)))

[1] "(1) Strongly disagree"          "(2) Disagree"                   "(3) Neither disagree nor agree" "(4) Agree"                      "(5) Strongly agree"            

  #if Agree or agree are detected at the beginning with a >2 level number assignment, or a >2 label number is detected:
  if (str_detect(labels(newlevels)[1],paste0('(',any(c(3:9)),')',sep="")) | str_detect(labels(newlevels)[1],paste0('Agree',sep="")) | str_detect(labels(newlevels)[1],paste0(' agree',sep="")) | any(str_detect(newlevels[[1]],paste0(c(3:9),sep="")))) {
    newlevels <- rev(newlevels)    
    test[,col] <- factor(test[,col], levels = c(labels(newlevels)), labels=c(unname(unlist(newlevels))))
    #test[,col] <- "Desired test successful"
    #addNA(col, ifany = any(is.na(col)))
    #print(str(unique(test[,col])))
    #print(labels(test[,col]))
  }

#Factorize and properly order all the predictors in this dataframe
test <- df
for (col in colnames(test)[13:ncol(test)]) {
  newlevels = list()
  newlabels = list()
  test[,col] <- df[,'assessment.personality.irritated_easily.enum']
  list_contents <- levels(test[,col])[which(!(is.na(levels(test[,col])) & is_empty(any(levels(test[,col]))) & identical(any(levels(test[,col])),character(0))))]
  chars <- seq(0,length(list_contents))
  if(!is.character(test[,col]) & !is.double(test[,col]) & length(levels(test[,col])[which(!is.na(levels(test[,col])))][which(str_detect(!(is.na(any(levels(test[,col]))) & is_empty(any(levels(test[,col]))) & identical(any(levels(test[,col])),character(0))), paste0("(",any(chars),")",sep="")))]) != 0) {
    print(paste0("factored column detected: ",'assessment.personality.irritated_easily.enum',sep=""))
    print(paste0("Testing character: ",chars,sep=""))
    list2<-list()
    for (i in seq(1,length(list_contents))) {
      list2<-list()
      char_name <- i
      list_item <- paste0(list_contents[which(str_detect(!(is.na(list_contents) & is_empty(list_contents) & identical(list_contents,character(0))), paste0("(",any(chars),")",sep="")))][i],sep="")
      if (!is.na(list_item)) {
        list1 <- as.numeric(char_name)
        names(list1) <- list(char =  list_item)
        list2 <- list.append(c(list(char = list_item),list2))
        names(list2) <- list(char =  names(list1))
        newlevels <- list.append(c(list1,newlevels))
        newlabels <- list.append(c(list2,newlabels))
      }
    }
  }
  if (any(str_detect(list_item,paste0(c(3:9),sep="")))) {
    for (j in seq(0,length(newlabels))) {
      newlabels %>%
        str_replace_all(paste0(length(newlabels)-j),newlabels[j],paste0(j+1))
    }
  }
  print(newlabels)
  #if Agree or agree are detected at the beginning with a >2 level number assignment, or a >2 label number is detected:
  if (str_detect(labels(newlevels)[1],paste0('(',any(c(3:9)),')',sep="")) | str_detect(labels(newlevels)[1],paste0('Agree',sep="")) | str_detect(labels(newlevels)[1],paste0(' agree',sep="")) | any(str_detect(newlevels[[1]],paste0(c(3:9),sep="")))) {
    newlevels <- rev(newlevels)    
    test[,col] <- factor(test[,col], levels = c(labels(newlevels)), labels=c(unname(unlist(newlabels))))
    #test[,col] <- "Desired test successful"
    #addNA(col, ifany = any(is.na(col)))
    #print(str(unique(test[,col])))
    #print(labels(test[,col]))
  } else if (str_detect(labels(newlevels)[1],paste0("isagree",sep="")) #Agree found at beginning
      & (labels(unname(unlist(newlevels)))[1] > 2) & (!str_detect(labels(newlevels)[1],paste0(' agree',sep=""))) | !str_detect(labels(newlevels)[1],paste0('Agree',sep=""))) {
      newlevels <- rev(newlevels)
      newlabels <- rev(newlabels)
    test[,col] <- factor(test[,col], levels = c(labels(newlevels)), labels=c(rev(unname(unlist(newlabels)))))
    #test[,col] <- "Desired test successful"
    #addNA(col, ifany = any(is.na(col)))
    print(str(unique(test[,col])))
  } else if ((str_detect(labels(newlevels)[1],paste0("Daily",sep=""))) #Agree found at beginning 
             & ((str_detect(labels(newlevels)[1],paste0('Often',sep=""))))) {
      newlevels <- rev(newlevels)
      newlabels <- rev(newlabels)
    test[,col] <- factor(test[,col], levels = c(labels(newlevels)), labels=c(rev(unname(unlist(newlabels)))))
    #test[,col] <- "Desired test successful"
    #addNA(col, ifany = any(is.na(col)))
    print(str(unique(test[,col])))
  } else if (str_detect(unname(unlist(newlevels))[[1]],paste0("isagree",sep=""))) {
     test[,col] <- factor(test[,col], levels = c(labels(newlevels)), labels=c(rev(unname(unlist(newlabels)))))
    #addNA(col, ifany = any(is.na(col)))
    print(str(unique(test[,col])))
  } else {
    print(paste0("Column is not factored",sep=""))
  }
}

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical
Warning in any(levels(test[, col])) :
  coercing argument of type 'character' to logical

[1] "factored column detected: assessment.personality.irritated_easily.enum"
[1] "Testing character: 0" "Testing character: 1" "Testing character: 2" "Testing character: 3" "Testing character: 4" "Testing character: 5"
$`(1) Strongly disagree`
[1] "(1) Strongly disagree"

$`(2) Disagree`
[1] "(2) Disagree"

$`(3) Neither disagree nor agree`
[1] "(3) Neither disagree nor agree"

$`(4) Agree`
[1] "(4) Agree"

$`(5) Strongly agree`
[1] "(5) Strongly agree"

df

df2 <- df
my_names <- names(df2)[-which((colnames(df2) == 'public_client_id') | (colnames(df2) == 'bowel') | (colnames(df2) == 'BMI_CALC') | (colnames(df2) == 'sex') | (colnames(df2) == 'age') | (colnames(df2) == 'eGFR') | (colnames(df2) == 'pss_4') | (colnames(df2) == 'pss_1') | (colnames(df2) == 'pss_2') | (colnames(df2) == 'pss_3') | (colnames(df2) == 'days_since_first_call') | (colnames(df2) == 'days_in_program'))]
pom <- list()  # initialize your pom
agg <- list()
#reference check of BMF variable from imported dataset - Mild Constipation vs 1,2,3,4
df2 <- within(df2, bowel <- relevel(bowel, ref = "High Normal"))

i = 0
dfOR = data.frame(matrix(ncol = 0, nrow = 7))
dfOR_ci = data.frame(matrix(ncol = 0, nrow = 7))
for(col in my_names){  # or seq_along(my_list)
  i = i + 1
  #print(col)
  pom[[col]] <- polr(factor(get(my_names[[i]])) ~ bowel + BMI_CALC + sex + age + eGFR, data=df2, Hess=TRUE, control=list(maxit=300))
  
  ## store table
  (ctable <- coef(summary(pom[[col]])))
  #print(ctable)

  ## calculate and store p values
  p <- pnorm(abs(ctable[, "t value"]), lower.tail = FALSE) * 2
  p <- p.adjust(p, method = "fdr", n = (length(df2) - 6))
  #print(p)
  ## combined table
  ctable <- cbind(ctable, "p value" = p)
  ci <- confint(pom[[col]]) # default method gives profiled CIs

  ## odds ratios
  #print(exp(coef(pom[[col]])))

  ## OR and CI
  dfOR_ci <- cbind(exp(cbind('variable' = coef(pom[[col]]), ci)),dfOR_ci)
  dfOR <- cbind('p value' = p[1:7],dfOR)

  #P value dataframe for all variables
  colnames(dfOR)[which((names(dfOR) == 'p value') | (names(dfOR) == '2.5 %') | (names(dfOR) == '97.5 %'))]   <- paste(c('p value','2.5 %', '97.5 %'),col,sep="-")

  #Odds Ratio & CI dataframe for all variables
  colnames(dfOR_ci)[which((names(dfOR_ci) == 'variable') | (names(dfOR_ci) == '2.5 %') | (names(dfOR_ci) == '97.5 %'))]   <- paste(c('variable','2.5 %', '97.5 %'),col,sep="-")
  
  #dfOR_ci <- data.frame(dfOR_ci)
  print(dfOR_ci)
  print(dfOR)
}

data1 <- dfOR_melt_p
header <- 'Stress'
Category <- vector(mode="character", length=nrow(data1))
data1 <- cbind(vector(mode="character", length=nrow(data1)),Category)
data1

#Plotting
backup <- dfOR_ci
dfOR_p <- dfOR
dfOR_cip <- cbind(dfOR_ci,dfOR_p)
dfOR_cip$variables <- rownames(dfOR_cip)

dfOR_cip$variables <- c('BMF constipated', 'BMF diarrhea', 'BMF low normal', 'BMI', 'Sex', 'Age', 'GFR')

dfOR_melt <- melt(data = dfOR_cip,
                  id.name = variables,
                variable.name = "ORCI",
                value.name = "value")

dfOR_melt_OR <- dfOR_melt %>% 
  filter(str_detect(ORCI, "^variable"))
dfOR_melt_97 <- dfOR_melt %>% 
  filter(str_detect(ORCI, "^97"))
dfOR_melt_25 <- dfOR_melt %>% 
  filter(str_detect(ORCI, "^2.5"))
dfOR_melt_p <- dfOR_melt %>%
  filter(str_detect(ORCI, "^p value"))

library(dplyr)
library(ggh4x)

dfOR_melt_OR$ORCI <- as.character(dfOR_melt_OR$ORCI)
dfOR_melt_97$ORCI <- as.character(dfOR_melt_97$ORCI)
dfOR_melt_25$ORCI <- as.character(dfOR_melt_25$ORCI)
dfOR_melt_p$ORCI <- as.character(dfOR_melt_p$ORCI)

ORCI <- function(data) {
  old_Category <- c()
  Category <- vector(mode="character", length=nrow(data))
  data <- cbind(data,Category)
  for (col in 1:nrow(data)) {
    header <- NULL
    if(str_detect(data[col,'ORCI'],'personality') | str_detect(data[col,'ORCI'],'satisfaction') | str_detect(data[col,'ORCI'],'joyful')
       | str_detect(data[col,'ORCI'],'pss') | str_detect(data[col,'ORCI'],'stress')) {
      header <- 'Psychological'
    } else if(str_detect(data[col,'ORCI'],'lifestyle') | str_detect(data[col,'ORCI'],'diet') | str_detect(data[col,'ORCI'],'pss')) {
      header <- 'Diet/Lifestyle'
    } else if(str_detect(data[col,'ORCI'],'health') | str_detect(data[col,'ORCI'],'vitals') | str_detect(data[col,'ORCI'],'digestion')) {
      header <- 'Health/Digestion'
    }
    if(!is_empty(header)) {
      data <- data %>% 
        mutate(old_Category = Category) %>%
        select(variables,ORCI,value,old_Category,Category) %>%
        mutate(Category = ifelse(grepl(data[col,'ORCI'],ORCI), header, old_Category))
    }
    data <- data %>%
      select(variables,ORCI,value,Category)
  }
  return(data)
}

dfOR_melt_OR <- ORCI(dfOR_melt_OR)
dfOR_melt_97 <- ORCI(dfOR_melt_97)
dfOR_melt_25 <- ORCI(dfOR_melt_25)
dfOR_melt_p <- ORCI(dfOR_melt_p)
dfOR_melt_OR
dfOR_melt_97
dfOR_melt_25
dfOR_melt_p


dfOR_melt_p$ORCI <- factor(dfOR_melt_p$ORCI)
dfOR_melt_p$Category <- factor(dfOR_melt_p$Category)
dfOR_melt_OR$ORCI <- factor(dfOR_melt_OR$ORCI)
dfOR_melt_OR$Category <- factor(dfOR_melt_OR$Category)
dfOR_melt_97$ORCI <- factor(dfOR_melt_97$ORCI)
dfOR_melt_97$Category <- factor(dfOR_melt_97$Category)
dfOR_melt_25$ORCI <- factor(dfOR_melt_25$ORCI)
dfOR_melt_25$Category <- factor(dfOR_melt_25$Category)
dfOR_melt_p$ORCI <- sub ("p value-","",dfOR_melt_p$ORCI)
dfOR_melt_OR$ORCI <-  sub("variable-", "", dfOR_melt_OR$ORCI)
dfOR_melt_97$ORCI <-  sub("97.5 %-", "", dfOR_melt_97$ORCI)
dfOR_melt_25$ORCI <-  sub("2.5 %-", "", dfOR_melt_25$ORCI)

#Plotting]
dfOR_melt_OR <- dfOR_melt_OR[complete.cases(dfOR_melt_OR[ ,c('ORCI')]),]
dfOR_melt_97 <- dfOR_melt_97[complete.cases(dfOR_melt_97[ ,c('ORCI')]),]
dfOR_melt_25 <- dfOR_melt_25[complete.cases(dfOR_melt_25[ ,c('ORCI')]),]
dfOR_melt_p <- dfOR_melt_p[complete.cases(dfOR_melt_p[ ,c('ORCI')]),]


dfOR_melt_OR
dfOR_melt_97
dfOR_melt_25
dfOR_melt_p


dfOR_melt_OR$significant <- dplyr::case_when(
  dfOR_melt_p$value <= 0.05  ~ TRUE,
  dfOR_melt_p$value > 0.05 ~ FALSE
)

dfOR_melt_OR$CI97 <- dfOR_melt_97$value
dfOR_melt_OR$CI25 <- dfOR_melt_25$value
dfOR_melt_OR$p <- dfOR_melt_p$value
dfOR_melt_OR

dfOR_melt_OR$CI97 <- dfOR_melt_97$value
dfOR_melt_OR$CI25 <- dfOR_melt_25$value
dfOR_melt_OR$p <- dfOR_melt_p$value
dfOR_melt_OR

df_unlabeled <- dfOR_melt_OR[which(dfOR_melt_OR$Category==''),]
old_Category <- c()
dfOR_melt_OR <- dfOR_melt_OR %>% 
  select(variables,ORCI,value,old_Category,Category,significant,CI97,CI25,p) %>%
  mutate(old_Category = Category) %>%
  mutate(Category = ifelse(str_detect(ORCI,'exercise'),'Diet/Lifestyle',
                          ifelse(str_detect(ORCI,'assessment.education.education.int'),'Psychological',
                           ifelse(str_detect(ORCI,'assessment.education.education.int'),'Psychological',
                            ifelse(str_detect(ORCI,'laxatives'),'Health/Digestion',
                             ifelse(str_detect(ORCI,'bowel_ease'),'Health/Digestion',
                              ifelse(str_detect(ORCI,'ab_pain'),'Psychological',
                               ifelse(str_detect(ORCI,'cooked_green_veg'),'Diet/Lifestyle',
                                ifelse(str_detect(ORCI,'daily_fruit'),'Diet/Lifestyle',
                                 ifelse(str_detect(ORCI,'season'),'Other',
                                  ifelse(str_detect(ORCI,'weekday'),'Other',
                                   ifelse(str_detect(ORCI,'days_since_first_draw'),'Other',
                                    ifelse(str_detect(ORCI,'month'),'Other',as.character(old_Category))))))))))))))
dfOR_melt_OR <- dfOR_melt_OR %>% 
  select(variables,ORCI,value,Category,significant,CI97,CI25,p)
dfOR_melt_OR

df_sig <- dfOR_melt_OR[which(dfOR_melt_OR$significant == TRUE & 
                               (dfOR_melt_OR$variables == 'BMF diarrhea' | 
                               dfOR_melt_OR$variables == 'BMF constipated' | 
                               dfOR_melt_OR$variables == 'BMF low normal')),]
df_sig[order(df_sig$p),]

df_psych <- dfOR_melt_OR[which(dfOR_melt_OR$Category == 'Psychological'),]
df_dietlife <- dfOR_melt_OR[which(dfOR_melt_OR$Category == 'Diet/Lifestyle'),]
df_healthdigest <- dfOR_melt_OR[which(dfOR_melt_OR$Category == 'Health/Digestion'),]

df_psych_BMF <- df_psych[complete.cases(df_psych[order(dfOR_melt_OR[which(df_psych$variables == 'BMF diarrhea' | df_psych$variables == 'BMF low normal' | df_psych$variables == 'BMF constipated'),][with(df_sig,order(Category,variables,p)),]$ORCI),]),]
df_psych_BMF <- df_psych_BMF[complete.cases(df_psych_BMF$significant == TRUE),]
df_psych_BMF_p <- df_psych_BMF[with(df_psych_BMF,order(p)),]
df_psych_BMF_p_select <- df_psych_BMF_p[df_psych_BMF_p$ORCI == 'ab_pain' | 
                                      df_psych_BMF_p$ORCI == 'assessment.joyful.moments.feel_empowered.enum'|
                                      df_psych_BMF_p$ORCI == 'assessment.satisfaction.rarely_rested.enum'|
                                      df_psych_BMF_p$ORCI == 'assessment.personality.irritated_easily.enum'|
                                      df_psych_BMF_p$ORCI == 'assessment.satisfaction.rarely_rested.enum'|
                                      df_psych_BMF_p$ORCI == 'assessment.personality.often_blue.enum',
]
df_psych_BMF_p_select

df_dietlife_BMF <- df_dietlife[complete.cases(df_dietlife[order(dfOR_melt_OR[which(df_dietlife$variables == 'BMF diarrhea' | df_dietlife$variables == 'BMF low normal' | df_dietlife$variables == 'BMF constipated'),][with(df_sig,order(Category,variables,p)),]$ORCI),]),]
df_dietlife_BMF <- df_dietlife_BMF[complete.cases(df_dietlife_BMF$significant == TRUE),]
df_dietlife_BMF_p <- df_dietlife_BMF[with(df_dietlife_BMF,order(p)),]
df_dietlife_BMF_p_select <- df_dietlife_BMF_p[df_dietlife_BMF_p$ORCI == 'assessment.lifestyle.vegetables.enum' | 
                                      df_dietlife_BMF_p$ORCI == 'assessment.lifestyle.water.enum'|
                                      df_dietlife_BMF_p$ORCI == 'assessment.lifestyle.cruciferous_vegetables.enum'|
                                      df_dietlife_BMF_p$ORCI == 'assessment.lifestyle.breakfast.enum'|
                                      df_dietlife_BMF_p$ORCI == 'assessment.diet.freq_cook_home.int'|
                                      df_dietlife_BMF_p$ORCI == 'assessment.diet.freq_raw_vegetables_salad.int'|
                                      df_dietlife_BMF_p$ORCI == 'assessment.lifestyle.sugary_drinks.enum'|
                                      df_dietlife_BMF_p$ORCI == 'exercise'|
                                      df_dietlife_BMF_p$ORCI == 'assessment.lifestyle.alcohol_days_a_week.enum',
]

df_dietlife_BMF_p_select

df_healthdigest_BMF <- df_healthdigest[complete.cases(df_healthdigest[order(dfOR_melt_OR[which(df_healthdigest$variables == 'BMF diarrhea' | df_healthdigest$variables == 'BMF low normal' | df_healthdigest$variables == 'BMF constipated'),][with(df_sig,order(Category,variables,p)),]$ORCI),]),]
df_healthdigest_BMF <- df_healthdigest_BMF[complete.cases(df_healthdigest_BMF$significant == TRUE),]
df_healthdigest_BMF_p <- df_healthdigest_BMF[with(df_healthdigest_BMF,order(p)),]
df_healthdigest_BMF_p_select <- df_healthdigest_BMF_p[df_healthdigest_BMF_p$ORCI == 'bowel_ease' | 
                                      df_healthdigest_BMF_p$ORCI == 'assessment.digestion.bowel.movement.completion.enum'|
                                      df_healthdigest_BMF_p$ORCI == 'laxatives'|
                                      df_healthdigest_BMF_p$ORCI == 'assessment.digestion.diarrhea.enum'|
                                      df_healthdigest_BMF_p$ORCI == 'assessment.digestion.bloating.enum'|
                                      df_healthdigest_BMF_p$ORCI == 'assessment.health.history.drugs_cholesterol.int'|
                                      df_healthdigest_BMF_p$ORCI == 'assessment.digestion.poor_or_lack_of_appetite.enum'|
                                      df_healthdigest_BMF_p$ORCI == 'assessment.digestion.gas.enum',
]

df_healthdigest_BMF_p_select

dfOR_melt_OR[which(dfOR_melt_OR$ORCI %in% df_psych_BMF_p_select$ORCI | 
                        dfOR_melt_OR$ORCI %in% df_dietlife_BMF_p_select$ORCI |
                        dfOR_melt_OR$ORCI %in% df_healthdigest_BMF_p_select$ORCI),]

psych <- ggplot(df_psych_BMF_p_select, aes(x = value, y = factor(variables, levels = c("Age","Sex","BMI",'GFR',"BMF diarrhea","BMF low normal", "BMF constipated")))) +
  facet_wrap(~ factor(ORCI)) +
  geom_point(data = df_psych_BMF_p_select, aes(color = Category)) +
  geom_errorbar(aes(color = df_psych_BMF_p_select$Category, xmin = df_psych_BMF_p_select$CI25, xmax = df_psych_BMF_p_select$CI97)) +
  geom_vline(xintercept = 1, linetype = "dashed", color = "black", size = 0.5) +
  ggtitle('Log-Odds Regression of Health/Digestion, Diet/Lifestyle, and Psychological Factors', subtitle = "Categorical Reference is High Normal BMF (7-21x/week)") +
  theme(plot.title = element_text(size=12),
        plot.subtitle = element_text(size=8),
        strip.text = element_text(size=5),
        legend.title = element_blank()) +
  geom_text(aes(label = ifelse(significant, "*", "")),position = position_dodge(width = .9), size = 14 / .pt) +
  scale_x_log10()+
  scale_y_discrete(name="Regression Variable", labels = c(
    "Age" = expression("Young"*symbol('\253')*"Old"),
    "Sex" = expression("Female"*symbol('\253')*"Male"),
    "BMI" = expression("Low BMI"*symbol('\253')*"High BMI"),
    "BMF constipated" = expression("High Normal BMF"*symbol('\253')*"Constipation"),
    "BMF low normal" = expression("High Normal BMF"*symbol('\253')*"Low Normal BMF"),
    "BMF diarrhea" =  expression("High Normal BMF"*symbol('\253')*"Diarrhea")))
psych

dietlife <- ggplot(df_dietlife_BMF_p_select, aes(x = value, y = factor(variables, levels = c("Age","Sex","BMI",'GFR',"BMF diarrhea","BMF low normal", "BMF constipated")))) +
  facet_wrap(~ factor(ORCI)) +
  geom_point(data = df_dietlife_BMF_p_select, aes(color = Category)) +
  geom_errorbar(aes(color = df_dietlife_BMF_p_select$Category, xmin = df_dietlife_BMF_p_select$CI25, xmax = df_dietlife_BMF_p_select$CI97)) +
  geom_vline(xintercept = 1, linetype = "dashed", color = "black", size = 0.5) +
  ggtitle('Log-Odds Regression of Diet, Lifestyle, and Stress/Pain Factors', subtitle = "Categorical Reference is High Normal BMF (7-21x/week)") +
  theme(plot.title = element_text(size=12),
        plot.subtitle = element_text(size=8),
        strip.text = element_text(size=5),
        legend.title = element_blank()) +
  geom_text(aes(label = ifelse(significant, "*", "")),position = position_dodge(width = .9), size = 14 / .pt) +
  scale_x_log10()+
  scale_y_discrete(name="Regression Variable", labels = c(
    "Age" = expression("Young"*symbol('\253')*"Old"),
    "Sex" = expression("Female"*symbol('\253')*"Male"),
    "BMI" = expression("Low BMI"*symbol('\253')*"High BMI"),
    "BMF constipated" = expression("High Normal BMF"*symbol('\253')*"Constipation"),
    "BMF low normal" = expression("High Normal BMF"*symbol('\253')*"Low Normal BMF"),
    "BMF diarrhea" =  expression("High Normal BMF"*symbol('\253')*"Diarrhea")))
dietlife

healthdigest <- ggplot(df_healthdigest_BMF_p_select, aes(x = value, y = factor(variables, levels = c("Age","Sex","BMI",'GFR',"BMF diarrhea","BMF low normal", "BMF constipated")))) +
  facet_wrap(~ factor(ORCI)) +
  geom_point(data = df_healthdigest_BMF_p_select, aes(color = Category)) +
  geom_errorbar(aes(color = df_healthdigest_BMF_p_select$Category, xmin = df_healthdigest_BMF_p_select$CI25, xmax = df_healthdigest_BMF_p_select$CI97)) +
  geom_vline(xintercept = 1, linetype = "dashed", color = "black", size = 0.5) +
  ggtitle('Log-Odds Regression of Diet, Lifestyle, and Stress/Pain Factors', subtitle = "Categorical Reference is High Normal BMF (7-21x/week)") +
  theme(plot.title = element_text(size=12),
        plot.subtitle = element_text(size=8),
        strip.text = element_text(size=5),
        legend.title = element_blank()) +
  geom_text(aes(label = ifelse(significant, "*", "")),position = position_dodge(width = .9), size = 14 / .pt) +
  scale_x_log10()+
  scale_y_discrete(name="Regression Variable", labels = c(
    "Age" = expression("Young"*symbol('\253')*"Old"),
    "Sex" = expression("Female"*symbol('\253')*"Male"),
    "BMI" = expression("Low BMI"*symbol('\253')*"High BMI"),
    "BMF constipated" = expression("High Normal BMF"*symbol('\253')*"Constipation"),
    "BMF low normal" = expression("High Normal BMF"*symbol('\253')*"Low Normal BMF"),
    "BMF diarrhea" =  expression("High Normal BMF"*symbol('\253')*"Diarrhea")))
healthdigest

df_full <- dfOR_melt_OR[which(dfOR_melt_OR$ORCI %in% df_psych_BMF_p_select$ORCI | 
                        dfOR_melt_OR$ORCI %in% df_dietlife_BMF_p_select$ORCI |
                        dfOR_melt_OR$ORCI %in% df_healthdigest_BMF_p_select$ORCI),]

full <- ggplot(df_full, aes(x = value, y = factor(variables, levels = c("Age","Sex","BMI",'GFR',"BMF diarrhea","BMF low normal", "BMF constipated")))) +
  facet_wrap(~ factor(ORCI, levels = c(
                                      'ab_pain',
                                      'assessment.joyful.moments.feel_empowered.enum',
                                      'assessment.satisfaction.rarely_rested.enum',
                                      'assessment.personality.irritated_easily.enum',
                                      'assessment.satisfaction.rarely_rested.enum',
                                      'assessment.personality.often_blue.enum',
                                      'assessment.lifestyle.vegetables.enum',
                                      'assessment.lifestyle.water.enum',
                                      'assessment.lifestyle.cruciferous_vegetables.enum',
                                      'assessment.lifestyle.breakfast.enum',
                                      'assessment.diet.freq_cook_home.int',
                                      'assessment.diet.freq_raw_vegetables_salad.int',
                                      'assessment.lifestyle.sugary_drinks.enum',
                                      'exercise',
                                      'assessment.lifestyle.alcohol_days_a_week.enum',
                                      'assessment.digestion.bowel.movement.completion.enum',
                                      'laxatives',
                                      'assessment.digestion.diarrhea.enum',
                                      'assessment.digestion.bloating.enum',
                                      'assessment.health.history.drugs_cholesterol.int',
                                      'assessment.digestion.poor_or_lack_of_appetite.enum',
                                      'assessment.digestion.gas.enum',
                                      'bowel_ease'), labels = c(
                                      'Abdominal Pain',
                                      'Joyful Moments\n Feel Empowered',
                                      'Satisfaction -\n Rarely Rested',
                                      'Personality -\n Irritated Easily',
                                      'Satisfaction -\n Rarely Rested',
                                      'Personality -\n Often Blue',
                                      'Vegetables in Diet',
                                      'Water Intake',
                                      'Cruciferous \nVegetables Intake',
                                      'Breakfast Intake',
                                      'Frequency of\n Cooking at Home',
                                      'Frequency of Raw\n Salad Vegetables',
                                      'Sugary Drinks Intake',
                                      'Exercise',
                                      'Alcohol -\n Days a Week',
                                      'Bowel Movement\n Completion',
                                      'Laxatives Usage',
                                      'Diarrhea Symptoms',
                                      'Bloating Symptoms',
                                      'Cholesterol Drugs History',
                                      'Poor/Lack of Appetite',
                                      'Gas Symptoms',
                                      'Ease of Bowel\nMovement')))+
  geom_point(data = df_full, aes(color = Category), size = 0.3) +
  geom_errorbar(aes(color = df_full$Category, xmin = df_full$CI25, xmax = df_full$CI97), size = 0.25) +
  geom_vline(xintercept = 1, linetype = "dashed", color = "black", size = 0.25) +
  ggtitle('Log-Odds Regression of Diet, Lifestyle, and Stress/Pain Factors', subtitle = "Categorical Reference is High Normal BMF (7-21x/week)") +
  theme(plot.title = element_text(size=10),
        plot.subtitle = element_text(size=8),
        strip.text = element_text(size=4),
        axis.text.y = element_text(size=3.75),
        axis.text.x = element_text(size=7),
        legend.title = element_blank()) +
  geom_text(aes(label = ifelse(significant, "*", "")),position = position_dodge(width = .9), size = 11 / .pt) +
  scale_x_log10()+
  expand_limits(y = c(0,length(levels(df_full$Category))+3)) +
  scale_y_discrete(name="Regression Variable", labels = c(
    "Age" = expression("Young"*symbol('\253')*"Old"),
    "Sex" = expression("Female"*symbol('\253')*"Male"),
    "BMI" = expression("Low BMI"*symbol('\253')*"High BMI"),
    "BMF constipated" = expression("High Normal BMF"*symbol('\253')*"Constipation"),
    "BMF low normal" = expression("High Normal BMF"*symbol('\253')*"Low Normal BMF"),
    "BMF diarrhea" =  expression("High Normal BMF"*symbol('\253')*"Diarrhea")))
full

#Final Figure
ggsave(
  "LogOddsRegressionvsDLS.png",
  plot = full,
  device = NULL,
  path = NULL,
  scale = 1,
  width = NA,
  height = NA,
  units = c("in", "cm", "mm", "px"),
  dpi = 300,
  limitsize = TRUE,
  bg = NULL
)

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